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CMaskedRangeSet Class Reference

Search Toolkit Book for CMaskedRangeSet

#include "masked_range_set.hpp"
(Private to src/app/blastdb.)

+ Inheritance diagram for CMaskedRangeSet:
+ Collaboration diagram for CMaskedRangeSet:

Public Member Functions

void Insert (int algo_id, const CSeq_id &id, const CSeq_loc &v)
 
virtual CMaskedRangesVectorGetRanges (const list< CRef< CSeq_id > > &idlist)
 Get ranges of masking data for the given Seq-ids. More...
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 

Private Types

typedef map< CSeq_id_Handle, CConstRef< CSeq_loc > > TAlgoMap
 

Private Member Functions

void x_FindAndCombine (CConstRef< CSeq_loc > &L1, int algo_id, CSeq_id_Handle &id)
 
CConstRef< CSeq_loc > & x_Set (int algo_id, CSeq_id_Handle id)
 

Static Private Member Functions

static void x_CombineLocs (CConstRef< CSeq_loc > &L1, const CSeq_loc &L2)
 

Private Attributes

CMaskedRangesVector m_Ranges
 
vector< TAlgoMapm_Values
 

Additional Inherited Members

- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Definition at line 46 of file masked_range_set.hpp.

Member Typedef Documentation

◆ TAlgoMap

Definition at line 66 of file masked_range_set.hpp.

Member Function Documentation

◆ GetRanges()

CMaskedRangesVector & CMaskedRangeSet::GetRanges ( const list< CRef< CSeq_id > > &  id)
virtual

Get ranges of masking data for the given Seq-ids.

Parameters
idSeq-ids for which to get masking data.
Returns
Masking data for these Seq-ids.

Implements IMaskDataSource.

Definition at line 39 of file masked_range_set.cpp.

References CConstRef< C, Locker >::Empty(), CRange_Base::GetFrom(), CSeq_id_Handle::GetHandle(), COpenRange< Position >::GetToOpen(), ITERATE, m_Ranges, NON_CONST_ITERATE, and x_FindAndCombine().

◆ Insert()

void CMaskedRangeSet::Insert ( int  algo_id,
const CSeq_id id,
const CSeq_loc v 
)
inline

◆ x_CombineLocs()

void CMaskedRangeSet::x_CombineLocs ( CConstRef< CSeq_loc > &  L1,
const CSeq_loc L2 
)
staticprivate

◆ x_FindAndCombine()

void CMaskedRangeSet::x_FindAndCombine ( CConstRef< CSeq_loc > &  L1,
int  algo_id,
CSeq_id_Handle id 
)
private

◆ x_Set()

CConstRef< CSeq_loc > & CMaskedRangeSet::x_Set ( int  algo_id,
CSeq_id_Handle  id 
)
private

Definition at line 96 of file masked_range_set.cpp.

References ctll::empty(), m_Ranges, and m_Values.

Referenced by Insert().

Member Data Documentation

◆ m_Ranges

CMaskedRangesVector CMaskedRangeSet::m_Ranges
private

Definition at line 68 of file masked_range_set.hpp.

Referenced by GetRanges(), and x_Set().

◆ m_Values

vector< TAlgoMap > CMaskedRangeSet::m_Values
private

Definition at line 69 of file masked_range_set.hpp.

Referenced by x_FindAndCombine(), and x_Set().


The documentation for this class was generated from the following files:
Modified on Wed May 29 18:38:08 2024 by modify_doxy.py rev. 669887